Seagrass beds occur globally and are substantial blue carbon sinks, yet factors that affect sediment organic carbon (SOC) sequestration are poorly characterized. We investigated the influences of eutrophication on SOC sequestration capacity in a mixed seagrass bed dominated by Thalassia hemprichii and Enhalus acoroides. We surveyed a tropical seagrass bed in the South China Sea along fish farming-induced gradients of nutrients to assess the variability of SOC content and composition in 30-cm-long sediment cores. No significant difference was observed for the SOC content and stock between the two species. Significantly higher microbial biomass carbon and SOC density were observed at the surface 3 cm layer under E. acoroides, and the longer roots of E. acoroides enhanced the seagrass contribution to the SOC near the root tip. SOC had a statistically lower concentration in the sediment layers where the seagrass roots primarily thrive close to fish farming, but greater exchangeable organic carbon was found in all the sediment layers as they approached fish farming. Nutrient enrichment markedly induced a larger ratio of labile C pools in almost all sediment layers. The mean SOC stock in the seagrass bed in Xincun Bay was 6.80 ± 1.03 Mg C/ha, and it showed insignificant variation along the nutrient gradient. Eutrophication may indirectly reduce the SOC sequestration capacity in the seagrass bed by enhancing labile organic carbon with a shorter resident time, and measures should be taken to reduce nutrient input into the seagrass bed to enhance its carbon sink.